Variant report

Variant	rs12893462
Chromosome Location	chr14:77812266-77812267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:77809100..77810943-chr14:77811490..77814273,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10132619	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1017186	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1046428	0.86[ASN][1000 genomes]
rs11845842	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11850308	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11850771	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12881799	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12886056	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12887558	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12894718	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1468951	0.86[ASN][1000 genomes]
rs17105724	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111700	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2160838	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2160839	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2160840	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2364155	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3759731	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56162150	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67845205	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7155184	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73311369	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73311375	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8005730	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9671248	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv902107	chr14:77790416-77871777	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12893462	TMED8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77789200-77818200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr14:77793200-77824600	Weak transcription	Psoas Muscle	Psoas
3	chr14:77801200-77812600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:77802000-77813000	Strong transcription	Primary B cells from peripheral blood	blood
5	chr14:77803600-77813000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr14:77803800-77835400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr14:77805200-77813000	Strong transcription	Fetal Intestine Large	intestine
8	chr14:77805200-77818600	Weak transcription	Small Intestine	intestine
9	chr14:77805400-77812800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr14:77805800-77813200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr14:77806200-77812800	Strong transcription	Thymus	Thymus
12	chr14:77806200-77819400	Weak transcription	A549	lung
13	chr14:77806400-77838600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr14:77806600-77822200	Weak transcription	NHDF-Ad	bronchial
15	chr14:77807800-77817600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr14:77807800-77819600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr14:77807800-77822000	Weak transcription	Osteobl	bone
18	chr14:77808000-77818800	Weak transcription	Placenta	Placenta
19	chr14:77808400-77812400	Weak transcription	HepG2	liver
20	chr14:77808400-77814200	Weak transcription	Esophagus	oesophagus
21	chr14:77808400-77818600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr14:77808400-77830600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr14:77808600-77819000	Weak transcription	NHEK	skin
24	chr14:77808800-77816000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr14:77809600-77817600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr14:77809600-77818000	Weak transcription	HMEC	breast
27	chr14:77809600-77825000	Weak transcription	Gastric	stomach
28	chr14:77809600-77842000	Weak transcription	HUVEC	blood vessel
29	chr14:77809800-77813600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:77809800-77814000	Weak transcription	Fetal Kidney	kidney
31	chr14:77809800-77814200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr14:77809800-77815600	Weak transcription	Brain Hippocampus Middle	brain
33	chr14:77809800-77815800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr14:77809800-77815800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr14:77809800-77816000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr14:77809800-77816000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr14:77809800-77816400	Weak transcription	Colon Smooth Muscle	Colon
38	chr14:77809800-77818600	Weak transcription	NH-A	brain
39	chr14:77809800-77818800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr14:77809800-77820200	Weak transcription	Brain Substantia Nigra	brain
41	chr14:77809800-77821200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr14:77810000-77815800	Weak transcription	Adipose Nuclei	Adipose
43	chr14:77810000-77815800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr14:77810000-77816000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr14:77810000-77816200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr14:77810000-77816200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr14:77810000-77816400	Weak transcription	Fetal Lung	lung
48	chr14:77810000-77818200	Weak transcription	Fetal Heart	heart
49	chr14:77810000-77820200	Weak transcription	Hela-S3	cervix
50	chr14:77810000-77838800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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